Sequencing of penguin genes gives family tree, presumed geographic origin, and hints about natural selection

August 20, 2020 • 9:00 am

A big group of researchers from around the world—science is truly international in this case—just published a paper in Proceedings of the National Academy of Sciences that involved sequencing the complete genome of 18 species of penguins as well as an outgroup, the southern giant petrel.  (Researchers differ on the number of extant penguin species, ranging from 17 to 20, as some populations are geographically isolated, making it hard to discern species status.)

The DNA information was combined with fossil data to yield a family tree of the living species, and also to reconstruct their evolutionary history, which suggested that the ancestor of all living and fossil penguins probably lived not in Antarctica, but on the coasts of Australia and/or New Zealand. Finally, the researchers were able to narrow in on a group of genes that may have undergone natural selection in the group, suggesting which adaptations were crucial for making a well-functioning penguin.

You can access the paper by clicking on the screenshot below, or see the pdf here. The full reference is at the bottom, and there’s a popular summary article at CNN.

I’ll try to be brief here. First, I’ve put below the family tree of living penguins deduced from the DNA information, with the divergence times that come from both DNA and fossil data. The radiation started around the beginning of the Miocene, roughly 22 million years ago.

As you can see, the largest species—the emperor and king penguins, form their own “outgroup” to the rest of the penguins, splitting off from the rest early in the group’s radiation but splitting from each other only about two million years ago. (Despite the radiation being old, most modern species split from their closest relatives only within the last few million years.)

The average temperature of the southern ocean is given by the graph in white and the scale on the left, with the dotted red line showing the beginning of the “strengthening” of the Antarctic Circumpolar Current (ACC), a strong ocean current that sweeps clockwise around Antarctica as seen from the South Pole, isolating the continent from warmer ocean temperatures to the north and allowing the ice sheet to persist.  A lot of the radiation followed the advent of this current’s new strength, which also coincided with the opening of the Drake Passage, creating a water gap between the previously connected land masses of Antarctica and South America.  It also produced a lot of sub-Antarctic islands that were also sites for colonization. And geographic isolation, possibly enforced by temperature, is an impetus for the formation of new species.

It was this stronger current and geographic separation that, the authors say, prompted new speciation events in penguins (most biologists assume that new species usually arise after populations become geographically separated). They did, however, detect some gene flow between penguin species, though it wasn’t extensive enough to wipe out the differences that produced this tree:

Using some assumptions and a complicated program, the authors could use the phylogeny to estimate the geographic range of the ancestral species as well as the ranges of ancestors within the phylogeny. Those are indicated with the letters A through I in the figure above.

The procedure is complicated, but it’s done the way evolutionists estimate ancestral traits of species—assuming that ancestors pass traits down to their descendants. In this case “geographic range” is considered a trait of a species. For example, if two closely related but distinct species occupy geographic areas that are close together, one can assume that their joint ancestor lived in that general area as well. The figure below shows the geographic areas that correspond the the letters of existing penguins (under their names) as well as the ancestors of groups (letters at the branch points).

The range of the ancestral node is letter I, and you can see that corresponds to the coastal areas of Australia and New Zealand, which, the authors assume, is where the ancestral species that gave rise to all modern penguins lived. This is a big conclusion of the paper, but since there are numerous assumptions that go into the biogeographic model, and not a lot of fossil data, I would take that conclusion as very tentative. If it’s true, that means that penguins evolved in areas where the water temperature at the time was abut 9ºC (48° F), and then some descendants (e.g. kings and adelies) colonized colder waters, while others (e.g.. Galápagos and African penguins) colonized warmer waters.

The ancestor of king and emperor penguins presumably lived on the coast of South America or Antarctica (letters A and C); kings currently breed on subantarctic islands and emperors only in Antarctica.

It’s possible, looking at the amount of genetic variation within whole genomes, to discern something about the demographic history (i.e., population sizes) of penguin species (again, there are some big assumptions here). You see below the plot of the “effective population size” (a figure that’s usually somewhat lower than the actual census size) for six species of penguins. Most show a strong drop in population size between about 70,000 and 40,000 years ago, which corresponds to the last glacial maximum (LGM, indicated by the vertical line). The authors say that the extreme cold during the LGM may have reduced the productivity of marine waters, and hence the abundance of fish and krill, the main diet of penguins.  That, in turn, is said to have reduced the population size of many penguin species:

Finally, there are ways to detect genes in a lineage that may have been subject to natural selection. This is done by finding genes in which there is an elevated rate of amino acid substitutions, which change the structure of a protein, over the rate of presumed “neutral” changes in DNA, which don’t change protein structure.  The assumption here, which is a good one, is that a relatively faster rate of protein evolution was promoted by natural selection.

Here’s a diagram of some of the genes, and classes of genes, that, says the analysis, underwent (positive) natural selection, presumably conferring adaptation on individuals in the various species. The genes that apparently evolved adaptively are in pathways influencing thermoregulation, osmoregulation via renal function (fluid and salt balance), blood pressure regulation (helps conserve oxygen and maintain core body temperatures), and oxygenation (important in deep diving). Some of the genes are named in the diagram below. Again, these genes are identified as candidates for adaptation only from their pattern of DNA substitution in the tree, and we don’t know for sure whether the changes really were adaptive, much less how they affected the animal.

The authors conclude on a sad note, saying that it took penguins millions of years to adapt to new temperatures (including colonizing the relatively warm waters around the Galápagos Islands), and thus would likely be unable to adapt to the relatively fast temperature increases accompanying global warming. While one would think that a history of slow adaptation doesn’t say anything about how fast adaptation could proceed under more rapid environmental change, we already know that global warming is seriously damaging some populations of penguins. The CNN report quotes the first author of the paper and describes some heartbreaking changes:

“Right now, changes in the climate and environment are going too fast for some species to respond to the climate change,” said Juliana Vianna, associate professor at the Pontifical Catholic University of Chile, in the UC Berkeley statement.

The different elements of climate change culminate in a perfect storm. Disappearing sea ice mean fewer breeding and resting grounds for emperor penguins. The reduced ice and warming oceans also mean less krill, the main component of the penguins’ diet.

The world’s second-largest emperor penguin colony has almost disappeared; thousands of emperor penguin chicks in Antarctica drowned when sea ice was destroyed by storms in 2016. Reoccuring storms in 2017 and 2018 led to the death of almost all the chicks at the site each season.

Some penguin colonies in the Antarctic have declined by more than 75% over the past 50 years, largely as a result of climate change.

In the Galapagos, penguin populations are declining as warm El Nino events — a weather phenomenon that sees warming of the eastern Pacific Ocean — happen more frequently and with greater severity. In Africa, warming waters off the southern coast have also caused penguin populations to drop drastically.

I’m lucky to have seen five species of penguins, including kings, on my trip to Antarctica last winter. It would break my heart if we humans, through our depredation of the environment, drove these magnificent products of evolution to extinction. They were here long before we were!

h/t: Matthew, Terrance

____________________

Vianna, J. A., F. A. N. Fernandes, M. J. Frugone, H. V. Figueiró, L. R. Pertierra, D. Noll, K. Bi, C. Y. Wang-Claypool, A. Lowther, P. Parker, C. Le Bohec, F. Bonadonna, B. Wienecke, P. Pistorius, A. Steinfurth, C. P. Burridge, G. P. M. Dantas, E. Poulin, W. B. Simison, J. Henderson, E. Eizirik, M. F. Nery, and R. C. K. Bowie. 2020. Genome-wide analyses reveal drivers of penguin diversification. Proceedings of the National Academy of Sciences:202006659.

A stunning case of mimicry

January 21, 2020 • 9:00 am

I don’t remember encountering this case of mimicry, but it’s so amazing that, when I became aware of it from a tweet (yes, Twitter has its uses), I decided to give it a post of its own.

First the tweet, sent to me by Matthew. He added, “This is the Iranian viper, as featured in Seven Worlds, One Planet, made by the BBC. Amazing.”

You don’t need to translate the Spanish, though, as the video below tells all. I swear that when I first watched it, I thought there was a real spider crawling on the snake’s back.

The snake is the spider-tailed horned viper, Pseudocerastes urarachnoides, which has a small range in Western Iran (map from Wikipedia):

It wasn’t described as a new species until 2006 in the paper below (free access); before that it was thought to be the already-describe Persian horned viper. (I guess they overlooked the tail ornament.)

Here’s a photo of the tail “spider” from the paper; the one below that is from Wikipedia. The resemblance may not be precise, but (as you see above), when the ornament is moved about, it looks remarkably like a spider—certainly good enough to fool birds.

In that paper, the authors didn’t know how the tail ornament was used, but were impressed at its spider-like appearance. And they guessed accurately:

This raises the question of the elaborate and sophisticated appearance of the caudal appendage in our new species, as the waving or wriggling motion of a distinctively colored tail tip seems perfectly adequate to attract lizard and anuran prey. We can only speculate that in the case of the present species, the caudal lure serves to deceive a more specific kind of prey, such as shrews or birds. Indeed, ZMGU 1300 [the specimen number] contains an undigested, unidentified passerine bird in the stomach (the feet protruding through the body wall).

Only later, using live captive specimens, did researchers see that the ornament did indeed attract birds that the snake caught and consumed, as in the video above.

Any biologist who sees this is immediately impressed by the ability of natural selection to mold not only morphology, but the behavior of the snake: the twitching of its tail so that the spider ornament appears to “walk.”  But any adaptation like this ornament must have incipient stages, and each subsequent modification must improve the adaptation—that is, it much give the snake possessing the “improved” improvement a reproductive advantage. (That advantage would derive from the better nutrition of a snake who caught more birds, and thus might have more offspring, increasing the proportion of genes for more spider-like ornaments.)

My own guess was that the ornament started with the simple twitching of the tail of an immobile snake, a twitching that might attract predators and, moreover, is already known in several snakes. After that, any mutation that modified the tail, making it look more like a spider, would give the snake a further reproductive advantage. And so we get the spider ornament, which might of course still be evolving. Concurrent with the evolution of the ornament itself would be the evolution of the snake’s tail-twitching behavior, which makes the caudal appendage resemble a spider nearly perfectly.

It turns out, of course, that I’m not the first person to think of this scenario. Discover Magazine wrote about this snake last spring, and speculated about its evolution:

“The evolution of luring is more complex than contrasting color or simple shaking — the movement is precisely adapted to duplicate prey movement frequencies, amplitudes and directions, at least in specialized cases.”It’s not uncommon for many snakes to do something similar with their tails to deceive prey. The common death adder of Australia buries itself in leaves, then writhes its tail like a worm to catch lizards and frogs. The Saharan sand viper conceals itself in sand with only its eyes and nostrils visible. When a lizard comes along, it sticks its tail out from the dirt, making it squirm like an insect larvae.  The behavior — and the elaborate body modifications that can accompany it — likely arose from a behavior common to many reptiles, Schwenk explains. When they are about to strike prey, any lizards and snakes enter a hyper-alert pose. The reptiles will focus their vision by cocking their heads to the side, arching their backs, and certain species will commonly vibrate their tail tip against the ground. This can distract the prey, which will shift its attention to the vibrating tail, ignoring the reptile mouth opening to grab them.“This simple pattern leads to selection causing refining of the tail form and motion to be more attractive to such prey by more accurately mimicking actual prey movements,” Schwenk theorizes. “The other ancestral condition that could have led to caudal luring, or possibly an intermediate step in the process, is the use of tail vibration for prey distraction rather than for luring.” Indeed, those most famous tail shakers, the rattlesnakes, sometimes also use caudal luring. For example, juvenile dusky pygmy rattlesnakes, whose rattle is so small it barely makes noise, wiggle their tails to attract prey. The behavior, in fact, may be key to how rattlesnakes evolved their distinctive rears, although this theory is somewhat controversial. “Like many other apparently simple things in biology, there is a lot of complexity to caudal luring that has barely been explored,” Schwenk says. “Much of this has been considered in a piecemeal fashion, but a thorough review and synthesis … has not been attempted.”

Now we’re not sure if this is the correct evolutionary pathway, but constructing a plausible step-by-step scenario like this, and showing that the intermediate “stages” occur as adaptations among existing species, is sufficient to refute the creationist claim that structures like the spider ornament could not have evolved and thus much have been created by God (or a “designer”, which means the same thing). The same kind of argument was used by Darwin in The Origin to refute Paley’s argument that the camera eye must have been created by God. Dawkins discusses it in the video below (and, as I recall, in his book The Blind Watchmaker).

 

Two biological puzzles

January 14, 2020 • 9:15 am

Here are two questions to ponder while I am doing other things today. The first comes from Matthew, whose words are indented:

Here’s a question which might be good to pose to readers.

Why are there no live-bearing birds? Live-birth has evolved many times in squamates, so is clearly within mutational reach of the reptilian genome (and interestingly, it generally leads to social behaviour). It has been argued that birds lay eggs because they would be too heavy to fly if they were carrying around young inside them. Apart from the obvious problem that bats manage fine, if that argument is right, you might expect some flightless birds to have been live-bearing. But they aren’t. Maybe they were in the past? Any hand-wavy explanations?

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And I have my own question:

Why are there no herbivorous snakes?  There are lots of snakes in the world and they slither in the grass, but none of them eat it—or any other vegetation. They are all carnivores.

This is particuarly puzzling in light of the fact that the relatives of snakes—lizards—often eat a great deal of vegetation, and at least one species—the marine iguana of the Galápagos—eats only vegetation (algae; though rarely they’ll eat other stuff). So it is possible for reptiles to evolve into herbivores. (Many of the dinosaurs were plant-eaters.) Why haven’t snakes done it?

Neither Matthew and I know the answers here (after all, these questions bear on mutational possibility, evolutionary history, physiology, and so on), but the questions are interesting to ponder. They do show that not all conceivable “niches” get filled by evolution.

Here’s a nice video of a marine iguana (Amblyrhynchus cristatus) foraging; I saw many of these when I visited the Galápagos some years ago. It is also the only marine lizard. There are other marine reptiles like saltwater crocodiles, sea snakes, and of course marine turtles, but to my knowledge this is the only lizard that forages in the sea (they live mostly ashore).

Nathan Lents on the imperfection of the human body (it’s evolution, of course)

January 10, 2020 • 12:45 pm

UPDATE:  I found out that the well-known evolutionary geneticist John C. Avise published a related book in 2010, but one that concentrates on a different line of evidence for evolution. John’s book (screenshot of cover below with link to Amazon) lays out the many suboptimal features of the human genome. He thus concentrates on molecular evidence, noting the many features in that bailiwick whose imperfection gives evidence for evolution and against intelligent design.  Lents’s and Avise’s books thus make a good pair, since the former seems to deal mostly with anatomy and physiology and the latter with molecular data. I’ll be reading both of them.

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Biologist Nathan Lents, whose abbreviated c.v. is given below, has been featured on this site before, both as a critic of creationism (good), but also as a defender of the Adam-and-Eve apologetics pushed by his religious friend Josh Swamidass (bad). But chalk up another two marks on Lents’s “good” side.  First, he’s written a book (click on screenshot below) that lays out all the suboptimal features of the human body—features whose imperfection gives evidence for evolution. I’m getting the book for teaching purposes, and here’s the Amazon summary:

Dating back to Darwin himself, the “argument from poor design” holds that examples of suboptimal structure/function demonstrate that nature does not have a designer. Perhaps surprisingly, human beings have more than our share of quirks and glitches. Besides speaking to our shared ancestry, these evolutionary “seams” reveal interesting things about our past. This offers a unique accounting of our evolutionary legacy and sheds new light on how to live in better harmony with our bodies, in all their flawed glory.

Nathan Lents is Professor of Biology at John Jay College and author of two recent books: Not So Different and Human Errors. With degrees in molecular biology and human physiology, and a postdoctoral fellowship in computational genomics, Lents tackles the evolution of human biology from a broad and interdisciplinary perspective. In addition to his research and teaching, he can be found defending sound evolutionary science in the pages of Science, Skeptic Magazine, the Wall Street Journal, The Guardian, and others.

And here’s a half-hour Center for Inquiry talk, clearly based on his book, in which Lents discusses how the flaws in the human body instantiate evolution. It’s not just that there are flaws—which support the notion that natural selection doesn’t produce absolute perfection, but simply the best result available given the existing genetic variation—but, more important: those flaws are understandable as the result of our evolution from ancestors who were different from us.

Some of Lents’s examples (like our broken gene in the Vitamin C synthesis pathway), are discussed in WEIT, but others, like the bizarre configuration of our nasal sinuses, aren’t. I haven’t seen the book, but it looks like a good compendium of evidence for evolution using something that everyone’s familiar with: the glitches and bugs in the human body.

It’s a good talk, and Lents is an energetic and lucid lecturer. I recommend that you listen to this, for you’ll learn stuff that will stay with you, and also serve to help you argue with creationists.

h/t: Michael

More about sexual selection in the New York Times

January 21, 2019 • 9:45 am

With the publication of his book The Evolution of Beauty (subtitle: How Darwin’s Forgotten Theory of Mate Choice Shapes the Animal World—and Us), Yale ornithologist Richard Prum gained an extraordinary amount of publicity in the popular press.  His theme was that “beauty”—that is, the evolution of extreme and stunning displays and ornamentation in male birds—results from a form of “runaway sexual selection” in which females’ random preference for extreme male traits produces amazing sexual dimorphism that has nothing to do with natural selection. (The peacock is perhaps the most famous example.) Prum’s book got two separate reviews in the New York Times, at least one other notice, and two big reportorial pieces, including recent the one below. The book was also nominated for a Pulitzer Prize for nonfiction, though it didn’t win.

Prum’s book is worth reading for two reasons. First, it presents a strong defense of the “runaway” model of sexual selection Prum calls it the “beauty happens” model, in which random female preferences lead to the exaggeration of male traits up to the point at which those traits actually hurt the male’s reproductive success (a peacock with a bigger tail would presumably not only be unable to fly, but would be a target for predators and find it hard to get around). Second some of Prum’s writing is very good, and his examples of exaggerated male behaviors and plumage engrossing and yet unknown to many laypeople.

But the book, as I’ve written before (see posts here), is tendentious. It ignores other models of sexual selection (except to denigrate them), it ignores the weaknesses of his own favored runaway model, and it misrepresents the views of evolutionary biologists (many of whom agree that the runaway may be important, but won’t buy into Prum’s view that it’s ubiquitous).  Prum claims that the runaway model is universally rejected by biologists in favor of “good genes” models (male traits indicate their genetic endowment). But that claim isn’t true: we just don’t have much data to distinguish all the competing models we have for how sexual selection works.

Further, Prum ties his model to progressive politics, saying that female choice in animals should hearten us because it shows that female “sexual autonomy” is natural. But such autonomy isn’t always present: many animals, for instance, have forced copulation. Bedbugs, for example, exhibit “traumatic insemination”, in which males bypass copulation by simply injecting sperm through the female body wall, with that sperm finding its way to the female eggs. Females don’t get to choose their mates, and copulation can actually kill them.

And there are many cases of forced and unwanted copulation by males, as well as male-male competition (viz., elephant seals) in which females are simply constrained to mate with whichever male wins a contest. Prum’s evocation of politics therefore demonstrates the “naturalistic fallacy”: that what happens in nature is what we should emulate. However, a lot of what happens in nature is stuff we shouldn’t emulate.

Prum also ties other models of sexual selection, including those in which a male’s traits indicate his vigor, health, or presence of “good genes”, to eugenics, and Nazi genocide, tarring the theories he doesn’t like with the social-justice cry of “Nazi”.  This is unconscionable. I can’t help but think, though, that Prum’s tying sexual selection to feminism was partly responsible for the book’s popularity and its Pulitzer nomination.

As I’ve written before, however, while Prum’s book received public approbation and good reviews—mostly from reviewers with no science background)—the reaction of the scientific community itself has been tepid and mostly critical for reasons I gave above. The three reviews I’ve read in scientific journals, including one by Gerald Borgia and Gregory Ball and another by Doug Futuyma, both highlight serious problem’s with Prum’s presentation, including the ignoring of alternative theories, the misrepresentation of the “beauty happens theory”, and the unwarranted connection between women’s rights and mate choice in birds. A more recent and much longer review, by Patricelli, Hebets, and Mendelson, published in Evolution (click on screenshot below for free access), was severely critical, and rightly so, though the authors did their best to be evenhanded and polite:

I’ve discussed this review before (full disclosure: I gave the authors some suggestions on a draft of their piece), and so won’t go over its contentions here. But if you want to read a review of Prum’s book—and one that is objective but critical—Patricelli et al. is the one to read. It is a good palliative for the publicity Prum gets repeatedly about his book.

That aside, several readers sent me the link to Ferris Jabr’s NYT piece above, suggesting that I write about it. I intended to, but was in Hawaii where I was having too much fun to work. Now that I’m back, I’ll summarize it as briefly as I can. (The piece is very long, and appeared in the NYT Sunday Magazine, an indication of how important the editors deemed the topic.)

Upshot:  Jabr’s piece is a mixed bag. (He’s a contributing writer to the New York Times and and often writes about science.)

The good bit is that Jabr at least indicates, as many writers haven’t, that the scientific community is lukewarm about The Evolution of Beauty and that Prum is somewhat dogmatic and dismissive of his critics. For example:

Despite his recent Pulitzer nomination, Prum still stings from the perceived scorn of his academic peers. But after speaking with numerous researchers in the field of sexual selection, I learned that all of Prum’s peers are well aware of his work and that many already accept some of the core tenets of his argument: namely that natural and sexual selection are distinct processes and that, in at least some cases, beauty reveals nothing about an individual’s health or vigor. At the same time, nearly every researcher I spoke to said that Prum inflates the importance of arbitrary preferences and Fisherian selection to the point of eclipsing all other possibilities. In conversation, Prum’s brilliance is obvious, but he has a tendency to be dogmatic, sometimes interrupting to dismiss an argument that does not agree with his own. Although he admits that certain forms of beauty may be linked to survival advantages, he does not seem particularly interested in engaging with the considerable research on this topic. When I asked him which studies he thought offered the strongest support of “good genes” and other benefits, he paused for a while before finally responding that it was not his job to review the literature.

Of course it was Prum’s job to review the literature, and especially to weigh his favored theory against alternatives, including “good genes” models and “sensory bias” models, in which female preference are not random but the byproduct of natural selection based on the species’ environment. How could it not be an author’s duty, when defending a theory, to review the literature for and against that theory?

Jabr also says this:

Like Darwin, Prum is so enchanted by the outcomes of aesthetic preferences that he mostly ignores their origins. Toward the end of our bird walk at Hammonasset Beach State Park, we got to talking about club-winged manakins. I asked him about their evolutionary history. Prum thinks that long ago, an earlier version of the bird’s courtship dance incidentally produced a feathery susurration. Over time, this sound became highly attractive to females, which pressured males to evolve adaptations that made their rustling feathers louder and more noticeable, culminating in a quick-winged strumming. But why, I asked Prum, would females be attracted to those particular sounds in the first place?

To Prum, it was a question without an answer — and thus a question not worth contemplating. “Not everything,” he said, “has this explicit causal explanation.”

Here Prum simply dismisses something that scientific reviewers mentioned repeatedly—where do female preferences come from? Prum assumes they are random, but there is a thriving field of sexual selection studying female preferences, showing how they might result from natural selection instead of just being “random” (i.e., aspects of neuronal wiring that have nothing to do with natural selection for the preference). Jabr also says, properly, that not all biologists have dismissed the runaway model, as Prum contends they have, but see it as one of a competing panoply of models that are hard to resolve. (Getting this kind of data from nature or even the lab is very difficult, and we weren’t there to see how sexual selection operated in the past.)

But in the rest of the article, Jabr seems to buy a lot of Prum’s contentions without properly evaluating the criticisms of other scientists. For example:

1.) The runaway model is not “Prum’s theory.” This model was first suggested by Ronald Fisher and elaborated and developed by scientists like Russ Lande and Mark Kirkpatrick. Yet Jabr repeatedly refers to the “beauty happens” model as “Prum’s theory”, as when he says that “Prum’s indifference to the ultimate source of aesthetic taste leaves a conspicuous gap in his grand theory.” (That statement is correct except that it’s not Prum’s grand theory.) This misleading attribution of the theory happens repeatedly. Let us be clear: Prum’s book is about presenting, defending, and applying a theory developed by other scientists.

2.) Jabr buys into Prum’s contention that sexual selection is fundamentally different from natural selection. Most biologists, I think, would disagree, seeing sexual selection as a subset of natural selection. That is, sexual selection is a form of selection based on female mate choice rather than other factors. But both sexual and natural selection involve enhancing those traits that affect reproductive success. (Jabr seems to mistake natural selection as a form of selection that enhances survival rather than reproductive success, but in fact the currency of all selection is the number of offspring that survive to spread your genes.). This may seem a semantic question, but both Jabr and Prum use this distinction to suggest that the runaway theory is a big and revolutionary improvement over previous notions of natural selection. This further inflates the runaway theory into something that it’s not.

In fact, natural and sexual selection blend into each other, and in some cases you can’t distinguish them. If a male produces sperm that swim faster than the sperm of other males in his species, and thus he gets more offspring, is this natural or sexual selection? It’s not based on mate choice, but does involve reproductive success. This is a form of male/male competition, analogous to those bull elk who butt horns during mating season, with the winner getting a harem of females. No female choice is involved in either case, but both could be seen as sexual selection. But they also represent natural selection—selection based on some individuals having traits (horns, fighting ability) that enables them to leave more genes.  My own judgment is that sexual selection is simply a subset of natural selection that involves mate choice, and not something fundamentally different.

3.) Jabr leaves out some aspects of Prum’s views that scientific critics have homed in on. Jabr doesn’t mention, for example, that Prum views the runaway model as the “null model” of sexual selection. That is, Prum deems it the model that we should accept unless we have good evidence for other models. But the runaway model isn’t null in that way: it does carry its own assumptions that themselves have to be justified and tested, such as female preference being “random” and not itself initially the result of natural selection or subject to stabilizing selection. The runaway assumes that male traits and female preferences are genetically correlated, and so on. No single model of sexual selection can be regarded as a “null model” to be regarded as a default option in the absence of any evidence.

4.) Jabr doesn’t fairly summarize the extent of scientific criticism of Prum’s book. While he does cite Borgia and Ball’s criticism, he neglects those of Futuyma and especially the thorough paper of Patricelli et al., and thus leaves out some important problems with Prum’s views (see below). Further, Jabr seems to have consulted critics at only the University of Texas at Austin, including my colleagues and friends Gil Rosenthal, Molly Cummings, and Mike Ryan. These people generally work on the sensory bias model of sexual selection, and thus emphasize theories different from Prum’s, but it would have been good to consult others who work on Prum’s model itself. These would include both Mark Kirkpatrick (also UT Austin!) and Russ Lande. I have talked to several “runaway” modelers, and their take is different from Prum’s: while they think the theory can operate, they are wary of its ubiquity in the absence of empirical evidence. This view, by the very proponents of Prum’s favorite model, shows a scientific caution far more admirable than Prum’s dogmatism.

5.) Jabr doesn’t mention at all an important aspect of Prum’s book: Prum’s view that because in some species females have “sexual autonomy” in choosing males, that hearten feminists who, rightfully, are against sexual coercion by human males. This omission by Jabr is a mistake, for this part of Prum’s message is one of its selling points, and surely explains some of the book’s popularity. But we shouldn’t buttress our morals by looking for parallels in nature, for, as I’ve said repeatedly, doing that makes our morality subject to revision via new information about nature. While some moral judgement can depend on empirical information (abortion may be one example), arguments about human rights and autonomy should be independent of how other species behave.

Jabr further ignores Prum’s invidious use of eugenics and comparisons to Nazis and genocide to tar models of sexual selection based on “good genes”. Ball and Borgia explicitly mention this, as do Patricelli et al. in the section of their review called “Birds and bedbugs make bad politics” (all three authors of that review are women).

My view then, is that Jabr’s summary of Prum’s work and the “beauty happens” theory is better than that of any of the summaries in popular venues, but still suffers from a general laziness manifested in contacting only scientists at UT Austin and in failing to summarize much of the criticism leveled by scientists at The Evolution of Beauty. Jabr didn’t do his scientific homework. The definitive popular critique of Prums’s views, as opposed to those that have already appeared in scientific journals, has yet to be written.

The results of sexual selection: male and female Manadrin Ducks (Aix galericulata). Photo from Wikipedia.

 

Natural selection against clueless cellphone users

November 4, 2018 • 1:45 pm

We’ve all seen people bump into telephone poles and nearly get hit by cars when walking around looking at their cellphones. (Hell, I’ve done it myself, at least with the telephone poles; I never look at a phone while crossing the street.) When I almost bumped into one of these metal poles in Paris, I realized that if they were a little shorter, and had a more injurious top than a simple ball, they could be used to select against heedless cellphone users.

The scenario: someone is walking along and looking at their cellphone, and bumps into a shorter version of one of these poles, say with a metal spike on top. Voilà! Their gamete-producing organs are injured, hurting their fertility. If there’s any genetic variation for using cellphones while oblivious to the external environment, that variation will be reduced by colliding with these “anti-gamete” poles. Within a generation, more people will be using their cellphones responsibly.

Of course this will work only for males, but that’s still selection on half the population, and presumably the genes for obliviousness are expressed in both sexes. Eventually only the nongenetic (socially conditioned) variation will remain.

My hand shows the height that the spikes needs to be; but of course it can be a foot or more in length, dealing with most of the height variation in human males.

Hangin’ on in the wind: Natural selection, hurricanes, and lizards

July 27, 2018 • 2:10 pm

by Greg Mayer

Colin Donihue at the Anolis Symposium, 17 March 2018.

At the Anolis Symposium at Fairchild Tropical Botanic Garden in March, one of the stars of the show was Colin Donihue of Harvard University, who gave a talk on the effect of last fall’s Hurricane Irma on Anolis scriptus, the endemic (and only native) anole of the Turks and Caicos. Colin and collaborators had chanced to visit and measure the morphology of the lizards just before the hurricane struck, and were able to return within weeks to see what had happened.

And something had happened. After Irma, the lizards had bigger toepads, longer arms, and shorter hind legs. The first two changes made sense—bigger toepads and longer arms are known to increase clinging ability in anoles– but the third seemed contrary to the first two. Longer legs would help them cling to the vegetation, and thus prevent them from being blown against the rocks or out to sea– so why did the ones with shorter legs survive better?

It was Colin’s exploration of this last question that made his talk one of the hits of the Symposium. In order to see the effect of Irma on the lizards, they used a garden leaf blower to simulate high winds, and recorded it all on video!

The video above is from Nature (not what Colin showed us in March), where the paper by Colin and colleagues will soon appear (already available online; there’s also a nice account of the field work by Colin at his website). What they have surmised, based on their leaf blower experiments, is that the hind legs of the lizards, once they’ve lost their grip on a perch, act as ‘sails’, catching the wind, and thus carrying the poor lizard away. “Yarr, ’tis an ill wind that blows a man out to sea.

What surprised me was that the lizards held on to the last with their arms—I would have thought that they would grasp with all fours, and that the hind legs, having a greater toepad surface area, would give out last. Perhaps the wind caught their (larger) hind legs around the perch, and forced them off first, presaging the eventual cause of blowing away altogether. As expected during a round of directional selection, the variances of traits generally decreased. Also, the body condition of the lizards was good—they weren’t starving after the hurricane, supporting the idea that the differential mortality occurred at the time of the storm.

So, what we have here is a nice demonstration of natural selection, and a plausible, experimentally supported cause of the differential survival. But it is important to note that this is not a demonstration of evolution by natural selection, and the reason for that is interesting, and relates to the fact that evolutionary biologists use the term ‘natural selection’ in a number of contexts.

While natural selection is a major cause of evolution, as Fisher noted in the first sentence of his Genetical Theory of Natural Selection, “Natural Selection is not Evolution.” A short definition of natural selection, and one that I have used in classes and in print is that natural selection is “consistent differential survival and reproduction of heritable variants.” That this does not equate to evolution by natural selection can be readily seen in the case of heterozygote advantage, such as sickle cell hemoglobin in malarial environments. In such cases, the result of natural selection is that the genetic composition of the population doesn’t change—rather, it reaches an equilibrium, and stays there. There’s no evolution.

But there’s another sense in which natural selection does not imply evolution, and that is the sense used in quantitative genetics, and also very often in studies of changes in quantitative phenotypic traits (such as the study under discussion). Quantitative genetics derives from the work of plant and animal breeders (which was an important source of facts and inspiration for Darwin), and one of its key results has long been summarized  in the ‘breeder’s equation‘:

R=sh²; or

Response to selection is equal to the selection differential times the heritability ()

What this means is that the evolutionary change due to natural selection depends on both how much the selected organisms differ from the mean of the population (the selection differential), and what proportion of that difference is passed on the offspring (the heritability). The heritability is where genetics comes in—the variants that are hereditary have a (non-zero) heritability.

The structure of the breeder’s equation flows naturally from how breeders work. First, they pick an animal to breed from, based on its possession of desirable variation (e.g., having larger breast muscles than average for a turkey). Then, they breed it. Finally, they check to see how much of the desirable variation is present in the offspring. If the offspring are exactly like the parent in the selected trait (i.e. desirable), then heritability is 100% or 1.0. If the offspring have only half the desirable advantage of the parent (say, being 4 ozs. larger than average, as opposed to 8 ozs. larger in the selected parents), then the heritability is 50% or .5. So in these two cases, selection leads to evolution. So where’s the problem?

The problem, or rather conceptual subtlety, is that the heritability may be 0—the offspring of the selected parents may not differ at all from the general mean of the population. Thus we can have selection, but no response to selection, and thus no evolution. So, although natural selection is often defined as I did above (consistent differential survival and reproduction of heritable variants), it is often the case that we can measure the differential survival before we know whether or not the variation is hereditary. And that’s what the breeder’s equation captures—the two-step nature of differential first, inheritance second.

The same two-step sequence of observation often applies in nature as well as on the farm or in the lab, and thus, ‘natural selection’ is often used in the sense of the differential, with the heritability evaluated separately (as it usually must be, since the observation of a phenotypic difference does not generally imply anything, one way or the other, about heritability).

As regards the measurement of selection differentials, Colin’s study has the very nice feature that the measurements were taken within the same generation; i.e. no reproduction had occurred—the second set of measurements were taken on lizards that had lived through the hurricane. This allows them to exclude certain other possible explanations—e.g., phenotypic plasticity—for the change in average morphology. A similar advantage accrued to the classic studies of natural selection in Darwin’s finches by the Grants and their collaborators. The Grants had the additional advantage that their birds were individually marked, so that the individual identities of surviving birds were known; on the Turks and Caicos, the same generation of adult lizards was sampled before and after the hurricane, and some individuals might indeed have been measured both times, but as the lizards were unmarked, individuals cannot be followed over time.

The next step for Colin is to return to the Turks and Caicos, to see if the morphological shifts persist into the next generation, thus supporting that evolution by natural selection has occurred—i.e., that the offspring resemble the selected (=surviving) parents. This could be complicated by the fact that, with the selective environmental force (Irma) now gone, there may be directional natural selection back toward the previous trait means. Thus, measuring the persistence of the observed change may be confounded by further changes occurring. As in the Darwin’s finches studies, a multi-year approach is called for.

The lizard traits that were studied are likely to be at least moderately heritable, as morphological features such as these are usually found to be so. There have been few studies of heritability in anoles, and there have been conflicting results. Using common garden experiments, Shane Campbell-Staton has found that critical thermal maximum, a physiological trait, is heritable in Anolis carolinensis; but Mike Logan has recently reported that heritability was low for other thermally-related traits in Anolis sagrei. Studies of the heritability of morphological traits in anoles should be a fruitful area of inquiry. One advantage the Grants had is that, using the information on pedigrees provided by individual marking, they measured the heritabilities of a number of quantitative phenotypic traits in the populations of Darwin’s finches they have studied.


Campbell-Staton, S.C., S.V. Edwards, and J B. Losos. 2016.Climate-mediated adaptation after mainland colonization of an ancestrally subtropical island lizard, Anolis carolinensis. Journal of Evolutionary Biology 29:2168-2180. link  (links marked ‘link’ may not be to full text)

Donihue, C.M., A. Herrel, A.-C. Fabre, A. Kamath, A.J. Geneva, T.W. Schoener, J.J. Kolbe and J.B. Losos. 2018. Hurricane-induced selection on the morphology of an island lizard. Nature in press. link

Fisher, R.A. 1930. The Genetical Theory of Natural Selection. Oxford University Press, Oxford. full text

Grant, P.R. and B.R. Grant. 2014. 40 Years of Evolution: Darwin’s Finches on Daphne Major Island. Princeton University Press, Princeton, New Jersey.

Logan, M.L., J.D. Curlis, A.L. Gilbert, D.B. Miles, A.K. Chung, J.W. McGlothlin, and R.M. Cox. 2018. Thermal physiology and thermoregulatory behaviour exhibit low heritability despite genetic divergence between lizard populations. Proceedings of the Royal Society B 285 (1878): 20180697. link

Mayer, G.C. and C.L. Craig. 2013. Theory of evolution. pp. 392-400 in S.A. Levin, ed. Encyclopedia of Biodiversity, 2nd ed., volume 3, Academic Press, Waltham, Mass.

Two remarkable cases of mimicry

May 30, 2017 • 8:45 am

Both of these cases were found by Matthew Cobb on Twi**er, and I’ve enlarged the photos at the bottom:

and

I think I’ve shown the buff-tip mothsh (Phalera bucephala) before; they are remarkable mimics of broken sticks when at rest. Now we’re not absolutely sure if this form of camouflage, presumably protecting the moths from predators, was the evolutionary impetus behind their appearance, but it seems likely, and could be tested in the lab with bird predators. I can’t think of any other explanation.

Here’s the adult with wings spread a bit (from Wikipedia):

Here’s the photo above, enlarged, clearly placed among broken sticks to show the mimicry:

Here’s another photo; note that the head is small, like the tip of a twig, and the legs are inconspicuously pressed down on the substrate. And of course its color and pattern are just like a broken twig:

Here’s the leaf katydid enlarged (the group is named in the tw**t above). It’s almost impossible for us to spot this: it even has a “rotten spot” mimicking those of leaves, as well as a yellowish body outline and a behavior that makes it place its front legs directly forward, looking like a leaf stem.  None of this would have evolved had the color, pattern, and behavior not given those individuals a selective advantage over less perfect mimics. This says something about the visual acuity of the predators and the power of natural selection.

I don’t know Latin, but I think the genus name, Phyllomimus, means “leaf mimic”.

 

The peppered moth – a video

April 7, 2017 • 8:26 am

by Matthew Cobb

The peppered moth story is one of the best examples of evolution in action. In this brief video, my final year student Tom Parry, tells the whole story, from 19th to 21st centuries. It includes interviews with my colleague Professor Laurence Cook, who carried out some of the recent research confirming how selection acts on the moth, and with Professor Ilik Saccheri of Liverpool University, who has identified the underlying genetic cause of this iconic change due to natural selection. PCC(E) makes a brief photographic appearance, due to the “notoriety” (his term) he attracted in 1998 because of this review.

As with Izzy Taylor’s video earlier this week, Tom needs your feedback – our students have to write a ‘reflective’ piece in which they discuss comments about their videos. So any comments you can make, either below or on YouTube would be gratefully received. If you are a teacher and want to use this with your students, feel free, but please try and collect some feedback from them.

 

A new paper showing the usefulness of the kin-selection model

February 4, 2016 • 9:45 am

There’s a new paper in the Proceedings of the National Academy of Sciences USA by David A. Galbraith et al. (free link and reference at bottom) that has a very cool result: one predicted by kin-selection theory. Kin selection, as you may know, is the idea that the adaptive value of a gene (and hence its evolutionary fate) must include information about how that gene affects its copies in relatives (e.g., a gene in parents for taking care of offspring can promote the replication of the copies that also occur in those offspring). Wikipedia describes this idea pretty succinctly.

Kin selection has been a very useful concept in understanding things like behaviors directed at offspring and relatives, and particularly in understanding the evolution of altruism and of one of its forms: eusociality—the behavior in which a colony of individuals is divided up into castes, some of which reproduce and some of which are nonreproductive but tend the “queen’s” brood (honeybees and naked mole rats are examples).

There are a few people, though, most notably Martin Nowak and E. O. Wilson at Harvard, who have questioned the usefulness of kin selection, arguing that group selection theory (or “multilevel” selection theory) is the only way to study the evolution of eusociality. I’ve written a lot on this site questioning their ideas (see some links below) as well as their claim that kin selection is not a useful way to study evolution in nature. The paper below, I think, shows the usefulness of the kin-selection paradigm, which seems to make predictions—ones that are verified—that don’t flow in any obvious way from a perspective of group or multilevel selection.

Because the paper is complex, I’ve asked my friend Phil Ward, a professor of entomology at the University of California at Davis (and a student of insect evolution) to explain its predictions and results. His explanation may be a bit difficult for non-biologists, but there is no simpler way to explain the study. Give it a go!


 

by Phil Ward

There has been a vociferous debate over the relative merits of group selection theory and inclusive fitness theory (or kin selection theory) as explanations for the evolution of altruistic behavior, especially following a contentious paper by Nowak et al. (2010) which claimed the superiority of the group selection approach. This was met with a resounding rebuff by a large group of evolutionary biologists who argued for the much greater explanatory power and heuristic value of inclusive-fitness thinking (e.g., Abbot et al. 2011). Some previous postings on WEIT about this topic have appeared here, here, here and here.

One fruitful area of inquiry in which kin selection theory makes explicit and testable predictions is in the study of genomic imprinting, a form of intragenomic conflict in which there is differential expression of genes inherited from the mother versus the father. In a theory paper published more than a decade ago, David Queller pointed out that this form of intragenomic conflict can be expected to be particularly widespread in colonies of social insects, and he employed kinship theory to predict the outcome of such conflict under different social contexts.

Now a recent empirical paper by Galbraith et al. (2016) provides convincing evidence that intragenomic conflict in honey bees indeed reveals itself in a way predicted by kin selection theory.

The authors first point out that genes inherited from mothers (matrigenes) and those inherited from fathers (patrigenes) are expected to be in conflict in honey bee workers that have an opportunity to reproduce. Why? Because a honey bee queen mates with multiple males, and the resulting workers are mostly half-siblings. These half-sibling individuals share half of their matrigenes but none of their patrigenes (see Figure 1 of the paper). So, consider a colony in which the queen has died, and half-sibling workers begin to compete over egg-laying (this behavior is inhibited by the queen while she is still alive). A worker’s matrigenes can be passed on when either she or her siblings reproduce, but her patrigenes are present only in her own offspring. Hence, as the authors put it, “compared with matrigenes, patrigenes will favor worker reproduction and exhibit enhanced activity on worker reproductive traits”.

This prediction was tested by quantifying the extent of genomic imprinting, i.e., the differential expression of genes of paternal origin.

The authors’ predictions were upheld. Using a series of genetic crosses that allowed them to distinguish matrigenes from patrigenes, they found that workers in queenless honey bee colonies showed greater expression of paternal than maternal genes, and this patrigene-biased expression was even higher in those workers that actually reproduced. In addition, when comparing parent-of-origin effects on reproductive traits such as ovary size and ovarian activity, patrigenes were shown to exert a much greater influence than matrigenes.

It should be emphasized that the worker reproduction occurring in queenless honey bee colonies produces only one sex: males.The workers lay unfertilized eggs and, as a consequence of the peculiar genetic system (haplodiploidy) found in bees, wasp and ants, these haploid eggs develop into males (which thus carry only one set of chromosomes). With no further production of workers, the colony will soon decline.

So, this last gasp of haploid reproductive effort that occurs when a queen dies (and is not replaced) will have selective significance only if the males that are produced have an opportunity to mate with queens from other colonies, something that takes place in population-wide mating swarms. Presumably this process of rearing and releasing drones (male bees) in a timely manner works best if some workers reproduce while the remainder continue to forage for food and feed the developing drone brood. Thus, colonies in which all reproductively capable workers give in to their patrigenic impulses might produce fewer reproductively successful drones than those in which there is some degree of reproductive restraint by the workers. One could argue that this is a kind of “colony-level” selection that weeds out disruptively high levels of patrigene expression, but inclusive fitness theory would explain this as a consequence of cost-benefit ratios that moderate the expression of both matrigenes and patrigenes.

Finally, for the small fraction of workers in a honey bee colony that are full siblings, the genetic interests of matrigenes and patrigenes are quite different: patrigenes can be equally well propagated through a worker’s own reproduction or that of a full sibling. Most competition for reproduction in honey bees is among half-siblings, however, so this should have little effect in honey bee colonies. Nevertheless, among other social insects in which the queen mates only once (such as bumble bees and many species of ants) all workers are full siblings and, as the authors note, the prediction is reversed: matrigenes should favor worker reproduction and show enhanced gene expression relative to patrigenes. Apparently this has not yet been studied, but it would constitute an elegant complementary test to the ground-breaking results of Galbraith et al.

9874
Honeybee workers surrounding their queen, who’s been marked with a dot

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Galbraith, D. A., S. D. Kocher, T. Glenn, I. Albert, G. J. Hunt, J. E. Strassmann, D. C. Queller, and C. M. Grozinger. 2016. Testing the kinship theory of intragenomic conflict in honey bees (Apis mellifera). Proc Nat. Acad Sci. USA 113:1020-1025. doi:10.1073/pnas.1516636113